Dear Marko,
I don't see where you build pmemd.cuda in your installation protocol
below. Are you certain that you are running the executable you think you
are running and not some other amber installation that is in your path?
Please look in the mdout file of one of your problematic pmemd runs for
the version it reports for pmemd.cuda. It should look something like this:
|--------------------- INFORMATION ----------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 12.X
|
| XX/XX/XXXX
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
| Duncan Poole (nVIDIA)
|
Please tell me what version number it reports and the date.
Thanks.
All the best
Ross
On 2/4/13 4:31 AM, "Marko Wehle" <Marko.Wehle.mpikg.mpg.de> wrote:
>
>Dear Amber Developers and Users,
>unfortunatly I've did not get any better behavior of Amber12 pmemd.cuda
>after minimzation steps.
>Here a list of working steps, to let you know what our protocol for
>installation is:
>
>###########################################
>
>tar xvfj Amber12.tar.bz2
>tar xvfj AmberTools12.tar.bz2
>
>cd $AMBERHOME
>./patch_amber.py --update-tree
>./patch_amber.py --update-tree
>./patch_amber.py --update-tree
>
># ./patch_amber.py --patch-level
>> Latest patch applied to AmberTools12: 33
>> Latest patch applied to Amber12: 14
>
>cd $AMBERHOME
>./configure gnu
>make -j 10 install
>
>#############################################
>
>Like described in the AMBER Bugfix section of the AMBER website, we have
>to run the patch script several times.
>Sincerely yours,
>Marko
>
>
>-----Ursprüngliche Nachricht-----
>Von: Marko Wehle
>Gesendet: Mi 30.01.2013 21:14
>An: amber.ambermd.org
>Betreff: Re: AMBER pmemd and pmemd.cuda, not restart files after
>minimization - fort.16 file instead
>>
>> Hello Amber Developers and Users,
>> I'm experiencing a behavior of the AMBER11 pmemd and pmemd.cuda version,
>> as well in AMBER12 pmemd.cuda, that is new to me.
>> They write out an empty restart file after minimization and put the
>>actual
>> coordinates in an fort.16 called file.
>> Simulations do fine.
>> After a search on the web I found the following entry:
>>
>> http://archive.ambermd.org/201207/0216.html
>>
>> that exactly describes this behavior.
>> The suggestion for solving the problem was recompiling AMBER11 with all
>> patches applied.
>> Unfortunately I could not find any further comments regarding this
>>issue.
>>
>
>bugfix.23 for Amber 11 and bugfix.7 for Amber 12 should fix this issue...
> You can use ./patch_amber.py --patch-level in Amber 12 to see which
>patches have been applied.
>
>
>> But what is irritating here, we've got this particular problem only
>>after
>> we applied all the patches while recompiling AMBER11 and AMBER12 last
>>week.
>> It concerns the pmemd.cuda in AMBER12 only, but in AMBER11 both pmemd
>>and
>> pmemd.cuda.
>> Before recompiling I did not observe this issues. The compile routine
>>and
>> the installation routine went fine so far and no errors were reported.
>>
>
>bugfix.1 for Amber 12 and bugfix.22 for Amber 11 actually introduced this
>issue, but I haven't seen them occur since the previous patches I
>mentioned
>were released.
>
>A temporary workaround is, of course, to use the fort.16 file instead (but
>that won't work particularly well in an automated workflow).
>
>Good luck,
>Jason
>
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Received on Mon Feb 04 2013 - 09:00:03 PST
